An ancient ship tumbles out of deep space, heading toward Babylon 5. The ship is broadcasting an automated message, identifying itself as the USS Copernicus.

In Downbelow, a human lurker begins to rant and rave, seemingly sensing something nearby. He looks out a porthole and sees the ancient ship approaching the station. This causes him to rave even more, desperately failing to recite the Lord's prayer, and he runs down the corridor screaming.

The Lurker, Amis, ends up in the Zocalo, shouting about "armies of darkness" and "soldiers of the devil." He accosts both Londo Mollari and G'Kar before Security Chief Michael Garibaldi quietly takes him into custody.

In C&C, Captain John Sheridan and Commander Susan Ivanova observe as maintenance bots are dispatched to the old ship. They are joined by Garibaldi a few moments later. Sheridan recognizes the design and writing of the ship. It is an old Earth sleeper ship, used for deep space exploration before they acquired jump gate technology: over 100 years ago. A single life sign is detected on the ship. Sheridan orders the ship brought into the station and links Dr. Franklin to join them in the docking bay.

Once on the station, Sheridan, Ivanova, Franklin, and Garibaldi come aboard. They find two cryostasis tubes. One of them contains a corpse, but the other contains a living woman. They open the tube and the woman is rushed quickly to Medlab. Along the way, she goes into cardiac arrest.

Back in security, Garibaldi checks on Amis, who is sleeping in a cell. Judging from the nightmares he is apparently having, Michael correctly assumes the Amis fought in the Earth-Minbari War. He mentions to one of the guards that he has had the same dream more than once.

Ivanova remains aboard the Copernicus. She is able to start up its computers. While aboard, she thinks she hears something.

Amis eventually wakes up in his cell. He cannot remember the earlier incident, so Garibaldi tells him what happened. Amis is embarrassed to admit it is not the first time. Garibaldi asks him about his service in the War, mentioning that he was a GROPO himself. He lets Amis leave, offering to put him touch with a counselor if he wants.

Dr. Franklin manages to revive the woman in Medlab. Ivanova, meanwhile, completes a diagnostic check and finds no malfunction of the second tube – its passenger should still be alive, meaning he was murdered.

Dr. Franklin performs an autopsy on the corpse, concluding that the victim died of organ failure: they are missing, with no trace of them aboard the ship. Garibaldi wants to immediately interrogate the living patient, but Franklin asks for some time to help her adjust. He goes to see her himself. She introduces herself as Mariah Cirrus, and explains that the other passenger is Will Cirrus, her husband, and that they volunteered for the exploration mission. Dr. Franklin informs her that she was stasis for over 100 years and that her husband is dead. Mariah is distraught, blaming herself for his death.

Amis wanders into the docking bay, seeing the Copernicus and seemingly recognizing it. He is soon seen and chased away by security.

Dr. Franklin escorts Mariah around the station, filling her in on some of the bigger events in Earth history. They bump into G'Kar, who suggests Mariah would be better off going back to when she came. Mariah suffers a vision, seeing herself in her tube with a strange, hostile force peering down at her. When it clears, she finds that she had blacked out. Dr. Franklin took her to his quarters, which were nearby. He explains that she seemed to be having a dream, a frightening one, as she cried out as though being attacked. He tells her that they suspect her husband was murdered. This upsets her greatly, but Dr. Franklin assures her she is not alone in all this. She tries to kiss him, but he pulls away. He tells her she needs rest, and she lies down on his couch.

Amis again races into the Zócalo rambling and screaming. Garibaldi is again on hand and confronts him. Amis mentions that the Copernicus brought a "Soldier of Darkness" to the station, a terrible entity he once faced during the War.

The lurker's body is brought to Medlab, where Dr. Franklin confirms he died in the same manner as Will Cirrus. Garibaldi tells Franklin and Sheridan about Amis. He explains that Amis was one of forty-seven men stationed to a small moon during the War, and that all the other members of his unit were slaughtered. Amis clearly believes that whatever wiped out his unit is now aboard. Tracing the ship's path, Garibaldi was able to confirm that the ship passed within the gravitational pull of exactly the same moon. Dr. Franklin is skeptical, and insists that Mariah could not have been involved in any case, as she spent the night at his quarters (on the couch). Nevertheless, Sheridan orders a 24 hour watch put on her. He mentions that word of the attack has leaked out and that a Council meeting has been called for.

Sheridan convenes a session of the Babylon 5 Advisory Council (though Delenn and Kosh are absent) and the League of Non-Aligned Worlds. The Markab Ambassador insists that Mariah has brought a Soldier of Darkness aboard the station. Londo is dismissive, but G'Kar is very interested. The Markab explains that a "great darkness" was defeated long ago, and when it happened it hid its agents throughout the galaxy: but now it is recalling them. Sheridan is not convinced, but agrees to do whatever he can to learn the truth – and stop whatever may be aboard.

Later that night, Garibaldi awakens suddenly. He decides to go to Amis and use him to try and track down whatever is aboard. Amis takes him into Downbelow, but is unable to pinpoint the monster. He talks to Garibaldi about his experience in the War, explaining that the Monster allowed him to live, as it had been feeding on him as a kind of snack. He is convinced it is aboard, and runs off alone to try and find it before Garibaldi can stop him.

Franklin finds Mariah aboard the Copernicus, reflecting on what has happened. She admits that she and Will were having problems, but wants to find justice for his killer. She explains that in her dreams, she is not alone in the cryo tube. She believes that whatever it was used her for food until it could find more – now it has an entire station to feed on.

Garibaldi tries to catch up to Amis and finds one of his garments. Then, a scream.

Garibaldi meets with Sheridan and Ivanova, going over Amis' account of what happened (despite the official records blaming the Minbari for the massacre). As Amis mentioned that the monster left a link to him, Garibaldi speculates that the same link may exist with Mariah.

Garibaldi approaches Mariah in Medlab. He asks her if she can help him find the monster. She admits the she can feel its presence and agrees to help him track it down. Franklin insists on going along.

In C&C, a report comes up about weapons fire in Brown Sector. Sheridan orders a full tactical team to meet him down there. Arriving in Brown Sector, they find Franklin treating an injured guard whom Garibaldi pulled out of a closed off sector. He then went back in alone. Sheridan and Ivanova lead the tactical team inside where they find Garibaldi (moments after he cornered the creature assaulting Amis). The Monster is almost completely invisible, and shrugs off PPG shots. Sheridan speculates that enough PPG blasts might be enough. Amis lures the monster out into the open, where it is killed by a massive crossfire from the tactical teams.

Amis is treated for minor injuries in Medlab. Mariah comes there, thanking Franklin for all his help. She has decided to return to Earth, needing time to heal and to grieve. She kisses him good-bye before leaving.

In C&C, Ivanova informs Sheridan that according to the Copernicus logs, the Soldier apparently was able to chart a course once it came aboard – the ship had been heading for Z'ha'dum before it detected Babylon 5 and automatically came there instead. Sheridan cannot believe this is merely a coincidence, and neither can Ivanova.

In his quarters, G'Kar opens the Book of G'Quan to a particular passage, one that depicts the very Soldier of Darkness.

"Hear me, O Lord, and the rest of you horrible sinners and you non-humanoids! Judgment day is coming and it don't care what you look like, 'cause I have seen it! Armies of darkness! Soldiers of the devil! Or something like that!"

– Amis in the Zócalo

“

"Now, unless you have a class C missionary license, it's time for a little R and R."

G'Kar had previously warned about an ancient enemy gathering its forces at Z'ha'dum (in "Revelations"). The Soldier the station personnel confront and eventually kill is likely an ally of the Shadows, given its appearance in the Book of G'Quan and its redirecting the Copernicus towards their homeworld.

This episode marks the first appearance of the Rangers. As Amis is preaching there is a Ranger watching him.

G'Kar's comment to Mariah: "The future isn't what it used to be" is a paraphrase of Yogi Berra, Hall of Fame baseball player, who said: "The future ain't what it used to be". It is one of his colorful "Yogi-isms".